- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 814c7f: Drop unused peek method (this used unencoded ids)
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 814c7f926dfe8d2aa344b5b17c83dcef757334d9 https://github.com/galaxyproject/galaxy/commit/814c7f926dfe8d2aa344b5b17c83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Drop unused peek method (this used unencoded ids) Commit: f3ba9e2b9e924cd94bc35e7bf5d5cfabb8e2fe48 https://github.com/galaxyproject/galaxy/commit/f3ba9e2b9e924cd94bc35e7bf5d5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge pull request #6796 from dannon/peek_drop [16.01] Drop unused peek method Commit: 482f1ea35971d6a0fe979e793119d207eca4b438 https://github.com/galaxyproject/galaxy/commit/482f1ea35971d6a0fe979e793119… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Commit: 8a1616aaf8160a4a7a7446b0cad072897c6eb568 https://github.com/galaxyproject/galaxy/commit/8a1616aaf8160a4a7a7446b0cad0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 Commit: 809ae58c52ed912a3256600ccf21456fac853782 https://github.com/galaxyproject/galaxy/commit/809ae58c52ed912a3256600ccf21… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into release_16.10 Commit: fa7f2a4f5c18ff6f3255a5230adc65508b5c9694 https://github.com/galaxyproject/galaxy/commit/fa7f2a4f5c18ff6f3255a5230adc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into release_17.01 Compare: https://github.com/galaxyproject/galaxy/compare/54b9b09fb2d2...fa7f2a4f5c18 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 814c7f: Drop unused peek method (this used unencoded ids)
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 814c7f926dfe8d2aa344b5b17c83dcef757334d9 https://github.com/galaxyproject/galaxy/commit/814c7f926dfe8d2aa344b5b17c83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Drop unused peek method (this used unencoded ids) Commit: f3ba9e2b9e924cd94bc35e7bf5d5cfabb8e2fe48 https://github.com/galaxyproject/galaxy/commit/f3ba9e2b9e924cd94bc35e7bf5d5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge pull request #6796 from dannon/peek_drop [16.01] Drop unused peek method Commit: 482f1ea35971d6a0fe979e793119d207eca4b438 https://github.com/galaxyproject/galaxy/commit/482f1ea35971d6a0fe979e793119… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Commit: 8a1616aaf8160a4a7a7446b0cad072897c6eb568 https://github.com/galaxyproject/galaxy/commit/8a1616aaf8160a4a7a7446b0cad0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 Commit: 809ae58c52ed912a3256600ccf21456fac853782 https://github.com/galaxyproject/galaxy/commit/809ae58c52ed912a3256600ccf21… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into release_16.10 Compare: https://github.com/galaxyproject/galaxy/compare/4a2814227cd7...809ae58c52ed **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 814c7f: Drop unused peek method (this used unencoded ids)
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 814c7f926dfe8d2aa344b5b17c83dcef757334d9 https://github.com/galaxyproject/galaxy/commit/814c7f926dfe8d2aa344b5b17c83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Drop unused peek method (this used unencoded ids) Commit: f3ba9e2b9e924cd94bc35e7bf5d5cfabb8e2fe48 https://github.com/galaxyproject/galaxy/commit/f3ba9e2b9e924cd94bc35e7bf5d5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge pull request #6796 from dannon/peek_drop [16.01] Drop unused peek method Commit: 482f1ea35971d6a0fe979e793119d207eca4b438 https://github.com/galaxyproject/galaxy/commit/482f1ea35971d6a0fe979e793119… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Commit: 8a1616aaf8160a4a7a7446b0cad072897c6eb568 https://github.com/galaxyproject/galaxy/commit/8a1616aaf8160a4a7a7446b0cad0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 Compare: https://github.com/galaxyproject/galaxy/compare/9a13a4af7fe4...8a1616aaf816 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 814c7f: Drop unused peek method (this used unencoded ids)
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 814c7f926dfe8d2aa344b5b17c83dcef757334d9 https://github.com/galaxyproject/galaxy/commit/814c7f926dfe8d2aa344b5b17c83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Drop unused peek method (this used unencoded ids) Commit: f3ba9e2b9e924cd94bc35e7bf5d5cfabb8e2fe48 https://github.com/galaxyproject/galaxy/commit/f3ba9e2b9e924cd94bc35e7bf5d5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge pull request #6796 from dannon/peek_drop [16.01] Drop unused peek method Commit: 482f1ea35971d6a0fe979e793119d207eca4b438 https://github.com/galaxyproject/galaxy/commit/482f1ea35971d6a0fe979e793119… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Compare: https://github.com/galaxyproject/galaxy/compare/dad5563cac85...482f1ea35971 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 814c7f: Drop unused peek method (this used unencoded ids)
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 814c7f926dfe8d2aa344b5b17c83dcef757334d9 https://github.com/galaxyproject/galaxy/commit/814c7f926dfe8d2aa344b5b17c83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Drop unused peek method (this used unencoded ids) Commit: f3ba9e2b9e924cd94bc35e7bf5d5cfabb8e2fe48 https://github.com/galaxyproject/galaxy/commit/f3ba9e2b9e924cd94bc35e7bf5d5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge pull request #6796 from dannon/peek_drop [16.01] Drop unused peek method Compare: https://github.com/galaxyproject/galaxy/compare/2207e7f8aa20...f3ba9e2b9e92 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] ff6526: Add 6789
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: ff65263ab2ee1351bbed11709d8536de694a5776 https://github.com/galaxyproject/galaxy/commit/ff65263ab2ee1351bbed11709d85… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6789 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] c51178: Four more PRs
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: c51178578dcf67c8dbe16d3d8320f660e0c80027 https://github.com/galaxyproject/galaxy/commit/c51178578dcf67c8dbe16d3d8320… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Four more PRs **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] b0dff4: allow making all datasets within history public, w...
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: b0dff4444085668cc3359b73d9d4d13b6da74cf6 https://github.com/galaxyproject/galaxy/commit/b0dff4444085668cc3359b73d9d4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/model/__init__.py M lib/galaxy/web/base/controller.py Log Message: ----------- allow making all datasets within history public, when sharing this is a one-off operation so notable behavior is that if you create a new dataset in the shared history, it still won't be public when there are default permissions set on history Commit: e4399021520440a8f58e33dbae161f031f8da9eb https://github.com/galaxyproject/galaxy/commit/e4399021520440a8f58e33dbae16… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/web/base/controller.py Log Message: ----------- show warning to user if some of the items within were not published Commit: 29a3b6bbfbde469e59f6a896dc8a4f76a8d3ea3d https://github.com/galaxyproject/galaxy/commit/29a3b6bbfbde469e59f6a896dc8a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/model/__init__.py M lib/galaxy/web/base/controller.py Log Message: ----------- Merge pull request #6793 from martenson/fix-sharing-by-link [18.09] allow making all datasets within history public, when sharing Compare: https://github.com/galaxyproject/galaxy/compare/5a98515df88b...29a3b6bbfbde **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 53b062: Add bam upload test
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 53b062f804c6d495b187656c84597f953210a2b0 https://github.com/galaxyproject/galaxy/commit/53b062f804c6d495b187656c8459… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Add bam upload test `test_upload_bam_file` fails on release_18.09 but passes on 18.05. Commit: 57fe3a741a9c3ac9c09513e21d44984ba046322e https://github.com/galaxyproject/galaxy/commit/57fe3a741a9c3ac9c09513e21d44… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Fix metadata spontaneuosly reverting Similar to https://github.com/galaxyproject/galaxy/pull/6631/files. This fixes https://github.com/galaxyproject/galaxy/issues/6769 Commit: 70e325574cb82be62b1be8090e714ce44441686b https://github.com/galaxyproject/galaxy/commit/70e325574cb82be62b1be8090e71… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Use with statement for all file uploads Commit: 5a98515df88b68483ad59bb7208a57f1a7f71664 https://github.com/galaxyproject/galaxy/commit/5a98515df88b68483ad59bb7208a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/model/metadata.py M test/api/test_tools_upload.py Log Message: ----------- Merge pull request #6789 from mvdbeek/fix_bam_upload [18.09] Fix bam upload resulting in 'auto' datatype Compare: https://github.com/galaxyproject/galaxy/compare/c5a325d01535...5a98515df88b **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/usegalaxy-playbook] 12f035: Main: mutable configs for Gemini install
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 12f035accb4d027ae548f415bdc89e1c07374a8f https://github.com/galaxyproject/usegalaxy-playbook/commit/12f035accb4d027a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_data_manager_conf.xml Log Message: ----------- Main: mutable configs for Gemini install **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0